Aggrey Suit, 49, an information and communications technology teacher on the graduate training programme at Blackheath Bluecoats school, south London, was discriminated against after suffering a suspected heart attack in September 2001, an employment tribunal ruled.
Mr Suit returned to work in June 2002 but his contract had been cut to two days a week. Although Mr Suit's GP said he could work full time from July, Kay Bickley, the head, who resigned last summer and now manages a guest house, insisted Mr Suit be given the all clear from Greenwich council's doctor first.
But deputy head Bob Henderson, who had a heart attack in December 2001 and returned to the 1,115-place school in Easter 2002, only had to provide a certificate from his GP.
Michael Hall-Smith, the tribunal's chairman, said: "We consider it appropriate to draw the inference that the reason for such difference in treatment was on the grounds of the applicant's race."
Despite pressure from the Association of Teachers and Lecturers and the Greenwich education department, Ms Bickley did not refer Mr Suit to occupational health until December 2002.
And, according to the tribunal, when she did so her letter cast doubt on Mr Suit's state of health.
Mr Suit, who was a minister for industry and technology in the Ugandan government between 1986 and 1991, said: "I was suicidal. I became an outcast in the school. There was a complete lack of trust between me and my employers. The pupils I was teaching could not respect me either."
Mr Suit, a father of four from Kent, did not return to full-time work until February 2003. He has been on sick leave with post-traumatic stress since July 2003.
A Greenwich council spokeswoman said the council had intervened and changed the management at the school.
She said: "Since this happened there has been a positive change in the ethos and teaching practices and standards have been raised.
"A black deputy head has been appointed at the school and we have also employed a head of year who is from an ethnic minority. We're sure that these new appointments will reassure parents that there is no discrimination at the school."
Four of Mr Suit's five claims that he had been racially discriminated against were not upheld at the tribunal.